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At least 289 records · Page 16Linked to original sources
PubMed1995

Modeling of radiogenic responses induced by fractionated irradiation in malignant and normal tissue.

The aim of this contribution is to outline how methods of system analysis, control theory and computer science can be applied to simulate malignant and normal cell growth and to optimize cancer treatment. Based on biological observations and cell kinetic data, our group has constructed three types of computer models: 1) A cell cycle model describing the spatial (3D) and temporal growth of tumor spheroids; 2) A compartment model describing the growth of rapidly proliferating normal cells; 3) A compartment model simulating slowly proliferating normal tissues. These growth models have been extended by an irradiation model based on the linear-quadratic survival function. Different clinical fractionation schemes (standard-, super-, hyperfractionation and weekly high single dose) have been applied to the tissues mentioned above. The simulation results show that in the case of irradiating a rapidly growing tumor spheroid the hyperfractionation (3 x 1-1.5 Gy per day) leads to a particularly good anti-tumor effectiveness. On the other hand, the radiogenic response of rapidly growing normal tissue to a hyperfractionated treatment schedule is severe. The same result is observed when simulating the late reaction on slowly growing parenchymal tissue. Therefore, this therapeutic modality is ensured only if the overall dose is reduced from DTOTAL = 60 Gy to DTOTAL = 50 Gy.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2005

Technologic advances in Robotic Surgery.

Medical science has achieved enormous accomplishments during the past couple of decades. These advances encompass the list of techniques involving manipulations of DNA and stem cells to minimally invasive techniques. The recent advances in integration of computer sciences, biomechanics and electronic miniaturization have made it possible to make the surgical techniques less invasive and highly precise. Much progress has been made in integrating robotic technologies with surgical instrumentation, as evident by thousands of successful robot-assisted surgical procedures. Such advances will enable continued progress in surgical instrumentation and, ultimately, surgical care.

Humans↗
PubMed2004

New approaches to shock and trauma research: learning from multidisciplinary exchange.

BACKGROUND: Our understanding of the complex network of pathophysiology after multiple injury is limited. It is proposed to overcome the limitations of the traditional linear reductionism approach by merging the expertise of biology and medicine with other disciplines such as mathematics, physics and computer science. METHODS: We organized a two-days-workshop, where surgeons and surgical scientists explained the problem from the medical (pathophysiological) perspective to a well selected group of German applied mathematicians and computer scientists. Vice versa they presented and discussed their approaches to complex system analysis. RESULTS AND CONCLUSIONS: Physicians found it difficult to develop questions and concepts that go beyond the classic mechanistic thinking. Well formulated questions are the most important prerequisites for successful application of mathematical tools. The possibilities and borders of Artificial Neural Networks (ANN), Hidden Markow Models (HMM), Agent Based Models (ABM), differential equations for problem solving were discussed. There is no master model for all aspects of pathophysiology, however, application of the models to specific problems is mandatory. CONCLUSIONS: Future breakthroughs can only be expected if we overcome language problems between disciplines. This cross talk was considered by all participants as a most important step.

Communication↗
PubMed1995

DNA solution of hard computational problems.

DNA experiments are proposed to solve the famous "SAT" problem of computer science. This is a special case of a more general method that can solve NP-complete problems. The advantage of these results is the huge parallelism inherent in DNA-based computing. It has the potential to yield vast speedups over conventional electronic-based computers for such search problems.

Computers↗
PubMed1995

[The rational computer-aided design of new drugs: a review of the methods].

Progress in computer science over recent 10 years has sharply reduced both the cost and the time spent on designing new drugs. Various concepts in solving this problem are now integrated into one approach--computer-assisted rational drug design. It consists of two groups of methods: 1) computer-assisted analysis of chemical structure-biological activity relationships by QSAR, OSMR, 3D QSAR and CoMFA; 2) computer modelling of the interaction of a ligand (a small drug molecule) with its target--a biological macromolecule, which is generally a protein. The findings of new ligands, which would selectively bind to the well-known protein can be done by screening the small molecules listed in some computer data bases. These new chemical structures can be used as a basis for drug designing.

Computer Simulation↗
PubMed1991

The role of a clinically based computer department of instruction in a school of medicine.

The evolution of activities and educational directions of a department of instruction in medical computer technology in a school of medicine are reviewed. During the 18 years covered, the society at large has undergone marked change in availability and use of computation in every aspect of medical care. It is argued that a department of instruction should be clinical and develop revenue sources based on patient care, perform technical services for the institution with a decentralized structure, and perform both health services and scientific research. Distinction should be drawn between utilization of computing in medical specialties, library function, and instruction in computer science. The last is the proper arena for the academic content of instruction and is best labelled as the philosophical basis of medical knowledge, in particular, its epistemology. Contemporary pressures for teaching introductory computer skills are probably temporary.

Computer User Training↗
PubMed2005

KEGG as a glycome informatics resource.

Bioinformatics approaches to carbohydrate research have recently begun using large amounts of protein and carbohydrate data. In this field called glycome informatics, the foremost necessity is a comprehensive resource for genome-scale bioinformatics analysis of glycan data. Although the accumulation of experimental data may be useful as a reference of biological and biochemical information on carbohydrates, this is insufficient for bioinformatics analysis. Thus, we have developed a glycome informatics resource (http://www.genome.jp/kegg/glycan/) in KEGG (Kyoto Encyclopedia of Genes and Genomes), an integrated knowledge base of protein networks, genomic information, and chemical information. This review describes three noteworthy features: (1) GLYCAN, a database of carbohydrate structures; (2) glycan-related pathways; and (3) Composite Structure Map (CSM), a map illustrating all possible variations of carbohydrate structures within organisms. GLYCAN includes two useful tools: an intuitive drawing tool called KegDraw, and an efficient glycan search and alignment tool called KEGG Carbohydrate Matcher (KCaM). KEGG's glycan biosynthesis and metabolism pathways, integrating carbohydrate structures, proteins, and reactions, are also a pivotal resource. CSM is constructed as a bridge between carbohydrate functions and structures. CSM is able to display, for example, expression data of glycosyltransferases in a compact manner. In all the KEGG resources, various objects including KEGG pathways, chemical compounds, as well as carbohydrate structures are commonly represented as graphs, which are widely studied and utilized in the computer science field.

Carbohydrates↗
PubMed1998

[Trends in genome informatics].

Genome Informatics is not only a new area of computer science for genome projects but also a new approach of life science. As the genome projects proceed, genome informatics is becoming more important to bio-industry as well as life science. The major subjects are as follows; Database technologies for integration of various kinds of biological data Knowledge discovery from the integrated databases Interpretation and analysis of DNA sequence data with the databases Computer technologies for simulating life system with knowledge extracted from the databases in order to check the validity of the knowledge In this article, the history and trend of development of computer technologies for the subjects are described except for computer simulation.

Animals↗
PubMed1997

DNA computing.

DNA computation is a novel and exciting recent development at the interface of computer science and molecular biology. We describe the current activity in this field following the seminal work of Adleman, who recently showed how techniques of molecular biology may be applied to the solution of a computationally intractable problem.

Algorithms↗
PubMed1989

The problem of carcinogenic hazard evaluation for new chemicals: general considerations about the carcinogenic process.

We discuss the problem of oncogenic hazard evaluation for new chemicals. In the recent past, assessment of global carcinogenicity in rodents was considered the most significant type of information. It has recently emerged that this type of information is not adequate to distinguish initiation and genotoxicity from promotion-like effects. In this report we suggest that hazards from initiating agents and hazards from promoting agents should be treated separately. In this perspective, longterm experiments for carcinogenicity in rodents should still play an important role but a less central one. Initiation-promotion experiments in different target organs are recommended. We suggest a strategy of hazard evaluation related to the initiating potential as distinct from overall carcinogenicity. The problem of utilizing not only the qualitative component of the available information, but also the quantitative component, is considered. Finally, we discuss a possible hazard evaluation for promoting effects, but conclude that this area is very much in its infancy. Possible contributions of computer science technology to the problem of oncogenic hazard evaluation are briefly introduced.

Animals↗
PubMed1997

Interest of image processing in cell biology and immunology.

Microscopy is a basic tool for cell biologists. Recent progress of electronics and computer science made powerful methodologies for digital processing of microscopic images easily available. These methods allowed impressive increase of the power of conventional microscopy. Dramatic image enhancement may be achieved by combination of filtering techniques, computer-based deblurring and contrast enhancement. Quantitative treatment of digitized images allows absolute determination of the density of different components of the observed sample, including antigens, intracellular calcium and pH. Morphometric studies are also greatly facilitated by image processing techniques. The capture of fast phenomena may be performed by transfer of small portion of microscopic images into computer memory as well as particular use of confocal microscopy. Finally, improved display of experimental data through coded colors or other procedures may enhance the amount of information that can be conveyed by visual examination of microscopical images. The purpose of the present review is to describe the basic principles of image processing and exemplify the power of this approach with a variety of illustrated applications to conventional, fluorescence or electron microscopy as well as confocal microscopy.

Image Processing, Computer-Assisted↗
PubMed2003

The future for computational modelling and prediction systems in clinical immunology.

Advances in computational science, despite their enormous potential, have been surprisingly slow to impact on clinical practice. This paper examines the potential of bioinformatics to advance clinical immunology across a number of key examples including the use of computational immunology to improve renal transplantation outcomes, identify novel genes involved in immunological disorders, decipher the relationship between antigen presentation pathways and human disease, and predict allergenicity. These examples demonstrate the enormous potential for immunoinformatics to advance clinical and experimental immunology. The acceptance of immunoinformatic techniques by clinical and research immunologists will need robust standards of data quality, system integrity and properly validated immunoinformatic systems. Such validation, at a minimum, will require appropriately designed clinical studies conducted according to Good Clinical Practice standards. This strategy will enable immunoinformatics to achieve its full potential to advance and shape clinical immunology in the future.

Allergens↗
PubMed2005

A multi-neighbor-joining approach for phylogenetic tree reconstruction and visualization.

The computationally challenging problem of reconstructing the phylogeny of a set of contemporary data, such as DNA sequences or morphological attributes, was treated by an extended version of the neighbor-joining (NJ) algorithm. The original NJ algorithm provides a single-tree topology, after a cascade of greedy pairing decisions that tries to simultaneously optimize the minimum evolution and the least squares criteria. Given that some sub-trees are more stable than others, and that the minimum evolution tree may not be achieved by the original NJ algorithm, we propose a multi-neighbor-joining (MNJ) algorithm capable of performing multiple pairing decisions at each level of the tree reconstruction, keeping various partial solutions along the recursive execution of the NJ algorithm. The main advantages of the new reconstruction procedure are: 1) as is the case for the original NJ algorithm, the MNJ algorithm is still a low-cost reconstruction method; 2) a further investigation of the alternative topologies may reveal stable and unstable sub-trees; 3) the chance of achieving the minimum evolution tree is greater; 4) tree topologies with very similar performances will be simultaneously presented at the output. When there are multiple unrooted tree topologies to be compared, a visualization tool is also proposed, using a radial layout to uniformly distribute the branches with the help of well-known metaheuristics used in computer science.

Algorithms↗
PubMed2003

Virtual patient simulator for distributed collaborative medical education.

Project TOUCH (Telehealth Outreach for Unified Community Health; http://hsc.unm.edu/touch) investigates the feasibility of using advanced technologies to enhance education in an innovative problem-based learning format currently being used in medical school curricula, applying specific clinical case models, and deploying to remote sites/workstations. The University of New Mexico's School of Medicine and the John A. Burns School of Medicine at the University of Hawai'i face similar health care challenges in providing and delivering services and training to remote and rural areas. Recognizing that health care needs are local and require local solutions, both states are committed to improving health care delivery to their unique populations by sharing information and experiences through emerging telehealth technologies by using high-performance computing and communications resources. The purpose of this study is to describe the deployment of a problem-based learning case distributed over the National Computational Science Alliance's Access Grid. Emphasis is placed on the underlying technical components of the TOUCH project, including the virtual reality development tool Flatland, the artificial intelligence-based simulation engine, the Access Grid, high-performance computing platforms, and the software that connects them all. In addition, educational and technical challenges for Project TOUCH are identified.

Artificial Intelligence↗
PubMed1998

Analysis of quantitative EEG with artificial neural networks and discriminant analysis--a methodological comparison.

Artificial neural networks (ANN) are widely used to solve problems of differentiating between groups. However, serious comparisons of this method with the traditional procedure for such tasks (discriminant analysis) are rare. Discussing the results of both methods with the example of highly topical data, we try to demonstrate advantages and drawbacks of both methods. For this purpose, quantitative EEGs of 78 alcoholics were investigated in order to determine whether it is possible to predict relapse of these patients at the beginning of treatment. ANN software is available in Kassel (Institute for Computer Sciences and Mathematics).

Alcoholism↗
PubMed1998

P/NP, and the quantum field computer.

The central problem in computer science is the conjecture that two complexity classes, P (polynomial time) and NP (nondeterministic polynomial time-roughly those decision problems for which a proposed solution can be checked in polynomial time), are distinct in the standard Turing model of computation: P not equal NP. As a generality, we propose that each physical theory supports computational models whose power is limited by the physical theory. It is well known that classical physics supports a multitude of implementation of the Turing machine. Non-Abelian topological quantum field theories exhibit the mathematical features necessary to support a model capable of solving all #P problems, a computationally intractable class, in polynomial time. Specifically, Witten [Witten, E. (1989) Commun. Math. Phys. 121, 351-391] has identified expectation values in a certain SU(2)-field theory with values of the Jones polynomial [Jones, V. (1985) Bull. Am. Math. Soc. 12, 103-111] that are #P-hard [Jaeger, F., Vertigen, D. & Welsh, D. (1990) Math. Proc. Comb. Philos. Soc. 108, 35-53]. This suggests that some physical system whose effective Lagrangian contains a non-Abelian topological term might be manipulated to serve as an analog computer capable of solving NP or even #P-hard problems in polynomial time. Defining such a system and addressing the accuracy issues inherent in preparation and measurement is a major unsolved problem.

Journal Article↗
PubMed2002

Protein design is NP-hard.

Biologists working in the area of computational protein design have never doubted the seriousness of the algorithmic challenges that face them in attempting in silico sequence selection. It turns out that in the language of the computer science community, this discrete optimization problem is NP-hard. The purpose of this paper is to explain the context of this observation, to provide a simple illustrative proof and to discuss the implications for future progress on algorithms for computational protein design.

Algorithms↗
PubMed1986

Prognostic factors in upper G.I. bleeding.

This presentation draws upon the experience of the O.M.G.E. Multi-national Upper G.I. Bleeding Survey, using data collected during 1980-1982 by 185 clinicians from 44 centres in 21 countries to discuss two questions. First, can prognostic factors be identified in patients presenting to hospital with upper G.I. bleeding, and if so what are they? Second, is it possible - by combining the two technologies of endoscopy and computers - to provide an individual patient with a short-term prognostic prediction sufficiently accurate to affect patient management. Amongst 4,010 patients, a number of clinical factors were found to affect short-term prognosis. These included patient age, previous history of heart or liver disease, confusion and dehydration on admission, jaundice, and ascites. Identification of the bleeding source via endoscopy was shown to aid short-term prognosis - especially in the period of the 2nd to 10th days post-admission. Use of computer analysis enabled "high risk" patients to be defined (of whom 63.8% suffered further bleeding and 30.0% died), and also a comparable "low risk" group (of whom only 4% suffered further bleeding and none died). Finally, "time-dependence" studies have been used to identify a group of patients who (by the 2nd day post-admission) have a residual risk of further bleeding sufficiently low (well under 1%) to suggest that considerable resources can be saved by the judicious use of endoscopy and computer science.

Age Factors↗